Parthiban Srinivasan

Abstracts

2 Artificial Intelligence in Bioscience: The Next Frontier

Authors: Parthiban Srinivasan

Abstract:

With recent advances in computational power and access to enough data in biosciences, artificial intelligence methods are increasingly being used in drug discovery research. These methods are essentially a series of advanced statistics based exercises that review the past to indicate the likely future. Our goal is to develop a model that accurately predicts biological activity and toxicity parameters for novel compounds. We have compiled a robust library of over 150,000 chemical compounds with different pharmacological properties from literature and public domain databases. The compounds are stored in simplified molecular-input line-entry system (SMILES), a commonly used text encoding for organic molecules. We utilize an automated process to generate an array of numerical descriptors (features) for each molecule. Redundant and irrelevant descriptors are eliminated iteratively. Our prediction engine is based on a portfolio of machine learning algorithms. We found Random Forest algorithm to be a better choice for this analysis. We captured non-linear relationship in the data and formed a prediction model with reasonable accuracy by averaging across a large number of randomized decision trees. Our next step is to apply deep neural network (DNN) algorithm to predict the biological activity and toxicity properties. We expect the DNN algorithm to give better results and improve the accuracy of the prediction. This presentation will review all these prominent machine learning and deep learning methods, our implementation protocols and discuss these techniques for their usefulness in biomedical and health informatics.

Keywords: Machine Learning, Health Informatics, Drug discovery, Deep learning, toxicity prediction

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1 Author Name Disambiguation for Biomedical Literature

Authors: Parthiban Srinivasan

Abstract:

PubMed provides online access to the National Library of Medicine database (MEDLINE) and other publications, which contain close to 25 million scientific citations from 1865 to the present. There are close to 80 million author name instances in those close to 25 million citations. For any work of literature, a fundamental issue is to identify the individual(s) who wrote it, and conversely, to identify all of the works that belong to a given individual. Due to the lack of universal standards for name information, there are two aspects of name ambiguity: name synonymy (a single author with multiple name representations), and name homonymy (multiple authors sharing the same name representation). In this talk, we present some results from our extensive work in author name disambiguation for PubMed citations. Information will be presented on the effectiveness and shortcomings of different aspects of successful name disambiguation such as parsing, validation, standardization and normalization.

Keywords: parsing, normalization, disambiguation, PubMed

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